1
|
Bakó I, Pusztai L, Pothoczki S. Outstanding Properties of the Hydration Shell around β-d-Glucose: A Computational Study. ACS OMEGA 2024; 9:20331-20337. [PMID: 38737074 PMCID: PMC11080014 DOI: 10.1021/acsomega.4c00798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 05/14/2024]
Abstract
Ab initio molecular dynamics (AIMD) simulations have been performed on aqueous solutions of four simple sugars, α-d-glucose, β-d-glucose, α-d-mannose, and α-d-galactose. Hydrogen-bonding (HB) properties, such as the number of donor- and acceptor-type HB-s, and the lengths and strengths of hydrogen bonds between sugar and water molecules, have been determined. Related electronic properties, such as the dipole moments of water molecules and partial charges of the sugar O atoms, have also been calculated. The hydrophilic and hydrophobic shells were characterized by means of spatial distribution functions. β-d-Glucose was found to form the highest number of hydrophilic and the smallest number of hydrophobic connections to neighboring water molecules. The average sugar-water H-bond length was the shortest for β-d-glucose, which suggests that these are the strongest such H-bonds. Furthermore, β-d-glucose appears to stand out in terms of the symmetry properties of both its hydrophilic and hydrophobic hydration shells. In summary, in all aspects considered here, there seems to be a correlation between the distinct characteristics of β-d-glucose reported here and its outstanding solubility in water. Admittedly, our findings represent only some of the important factors that influence the solubility.
Collapse
Affiliation(s)
- Imre Bakó
- HUN-REN
Research Centre for Natural Sciences, Magyar tudósok körútja 2., H-1117 Budapest, Hungary
| | - László Pusztai
- HUN-REN
Wigner Research Centre for Physics, Konkoly-Thege M. út 29-33., H-1121 Budapest, Hungary
- International
Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Szilvia Pothoczki
- HUN-REN
Wigner Research Centre for Physics, Konkoly-Thege M. út 29-33., H-1121 Budapest, Hungary
| |
Collapse
|
2
|
Masella M, Léonforté F. Chitosan Polysaccharides from a Polarizable Multiscale Approach. ACS OMEGA 2023; 8:35592-35607. [PMID: 37810703 PMCID: PMC10551911 DOI: 10.1021/acsomega.3c01584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/30/2023] [Indexed: 10/10/2023]
Abstract
We report simulations of chitosan polysaccharides in the aqueous phase, at infinite dilute conditions and zero ionic strength. Those simulations are performed by means of a polarizable multiscale modeling scheme that relies on a polarizable all atom force field to model solutes and on a polarizable solvent coarse grained approach. Force field parameters are assigned only from quantum chemistry ab initio data. We simulate chitosan monomer units, dimers and 50-long chains. Regarding the 50-long chains we simulate three sets of ten randomly built chain replica at three different pH conditions (corresponding to different chain protonation states, the chain degree of deacetylation is 85%). Our simulations show the persistence length of 50-long chitosan chains at strong acidic conditions (pH <5) to be 24 ± 2 nm (at weak/negligible ionic strength conditions), and to be 1 order of magnitude shorter at usual pH conditions. Our simulation data support the most recent simulation and experimental studies devoted to chitosan polysaccharides in the aqueous phase.
Collapse
Affiliation(s)
- Michel Masella
- Laboratoire
de Biologie Bioénergétique, Métalloprotéines et Stress, Service de Bioénergétique,
Biologie Structurale et Mécanismes, Institut Joliot, CEA Saclay, Gif sur Yvette Cedex F-91191, France
| | - Fabien Léonforté
- L’Oréal
Group, Research & Innovation, Aulnay-Sous-Bois 93600, France
| |
Collapse
|
3
|
Jaeschke SO, Lindhorst TK, Auer A. Between Two Chairs: Combination of Theory and Experiment for the Determination of the Conformational Dynamics of Xylosides. Chemistry 2022; 28:e202201544. [PMID: 35754398 PMCID: PMC9804333 DOI: 10.1002/chem.202201544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Indexed: 01/05/2023]
Abstract
The conformational properties of monosaccharides constitute fundamental features of oligosaccharides. While the energy landscape of monosaccharides can be altered by a specific biochemical environment or by chemical modifications, the analysis of resulting dynamic conformational equilibria is not feasible by experimental means alone. In this work, a series of β-d-xylopyranosides is used to outline how a combination of experimental NMR parameters and computed molecular properties can be used to determine conformers and quantify the composition of conformational equilibria. We demonstrate that identifying the most stable conformers using energy calculations is challenging and computing of NMR shieldings is typically not sensitive enough. On the other hand, computed spin-spin coupling constants for the xyloside ring can be used to unambiguously assign experimental NMR data of dynamic conformational equilibria and quantify the ratio of different conformers in the mixture. As a proof of principle, this procedure allowed to analyze a hitherto unknown dynamic equilibrium of a diamino-xyloside as a precursor of a molecular switch.
Collapse
Affiliation(s)
- Sven Ole Jaeschke
- Otto Diels Institute of Organic ChemistryChristiana Albertina University of KielOtto-Hahn-Platz 3–424118KielGermany
| | - Thisbe K. Lindhorst
- Otto Diels Institute of Organic ChemistryChristiana Albertina University of KielOtto-Hahn-Platz 3–424118KielGermany
| | - Alexander Auer
- Max-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470Mülheim an der RuhrGermany
| |
Collapse
|
4
|
Tanaka S, Tsenkova R, Yasui M. Details of glucose solution near-infrared band assignment revealed the anomer difference in the structure and the interaction with water molecules. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114764] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
5
|
Prokhorov E, Luna-Barcenas G, Kumar-Krishnan S, Mauricio Sánchez R, Castillo Reyes B, Hernández Vargas J. Probing molecular interactions of polysaccharides in the presence of water. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
6
|
Yang Y, Liu G, Tu Z, Wang H, Hu Y, Mao J, Zhang J. Insight into the Mechanism of Reduced IgG/IgE Binding Capacity in Ovalbumin as Induced by Glycation with Monose Epimers through Liquid Chromatography and High-Resolution Mass Spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:6065-6075. [PMID: 32396375 DOI: 10.1021/acs.jafc.0c01233] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ovalbumin (OVA) is one of the major food allergens in hen eggs. In this work, it was demonstrated that glycation with d-glucose and its epimers, including d-mannose, d-allose, d-galactose, and l-idose, could effectively attenuate the IgG/IgE binding of OVA, which was attributed to the covalent masking by sugars and to its structural changes. The glycation sites were determined, and their average degree of substitution was found using liquid chromatography coupled with high-resolution mass spectrometry. Fluctuations in OVA conformation were monitored by conventional spectrometry. Compared to those of OVA-Man and OVA-Glu, OVA-All, OVA-Gal, and OVA-Ido showed a higher glycation extent, and the alterations on their steric layouts were more drastic, suggesting that the configuration of hydroxyl groups at positions C-3, C-4, and C-5 in sugars might be important for the glycation reactivity; as such, their capabilities in binding with IgG/IgE decreased more significantly. Attempts were made to provide valuable information for in-depth understanding of the differences in biochemical functionality among epimeric sugars. These insights would be helpful for designing sweetened food products with a desirable level of safety.
Collapse
Affiliation(s)
- Yipeng Yang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, China
| | - Guangxian Liu
- Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi 330200, China
| | - Zongcai Tu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, China
- Engineering Research Center of Freshwater Fish High-Value Utilization of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang, Jiangxi 330022, China
| | - Hui Wang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, China
| | - Yueming Hu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, China
| | - Jihua Mao
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, China
| | - Jingjing Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, China
| |
Collapse
|
7
|
de la Concepción JG, Martínez RF, Cintas P, Babiano R. Mutarotation of aldoses: Getting a deeper knowledge of a classic equilibrium enabled by computational analyses. Carbohydr Res 2020; 490:107964. [PMID: 32163730 DOI: 10.1016/j.carres.2020.107964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/23/2020] [Accepted: 02/26/2020] [Indexed: 10/24/2022]
Abstract
The mutarotation equilibrium, by which reducing carbohydrates exist in solution as the α and β anomers of cyclic (furanoid and pyranoid) structures, along with open-chain (aldehyde and hydrate) forms, and whose ratios are depending on factors such as temperature, pH and solvent, portraits a phenomenon involved in numerous processes of chemical and biological importance. Herein, we have developed a DFT-based rationale that provides a broader landscape for anomerizations and ring-open chain interconversions, together with the pivotal role exerted not only by the aldehyde intermediate (essentially the only acyclic structure taken into account so far), but also the hydrate form (often more abundant at the equilibrium). These calculations reveal a more complex and richer scenario than was thought, and identify different mutarotation mechanisms that hinge on every monosaccharide. It is noteworthy that pyranose-furanose interconversion may actually occur without the intermediacy of open-chain forms. For the aldoses evaluated, namely d-glucose, d-ribose, and d-xylose, all structures involved in mutarotation undergo interconversion pathways, whose energy barriers calculated at the M06-2X/6-311++G(d,p) level, are in good agreement with previous experimental measurements.
Collapse
Affiliation(s)
- Juan García de la Concepción
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX and IACYS-Unidad de Química Verde y Desarrollo Sostenible, E-06006, Badajoz, Spain.
| | - R Fernando Martínez
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX and IACYS-Unidad de Química Verde y Desarrollo Sostenible, E-06006, Badajoz, Spain
| | - Pedro Cintas
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX and IACYS-Unidad de Química Verde y Desarrollo Sostenible, E-06006, Badajoz, Spain
| | - Reyes Babiano
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias-UEX and IACYS-Unidad de Química Verde y Desarrollo Sostenible, E-06006, Badajoz, Spain.
| |
Collapse
|
8
|
Tautomeric and epimeric equilibria of aldo- and ketohexoses studied by the MD simulations and QM calculations. Carbohydr Res 2019; 474:8-15. [DOI: 10.1016/j.carres.2019.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/04/2019] [Accepted: 01/09/2019] [Indexed: 11/17/2022]
|
9
|
Lee KH, Schnupf U, Sumpter BG, Irle S. Performance of Density-Functional Tight-Binding in Comparison to Ab Initio and First-Principles Methods for Isomer Geometries and Energies of Glucose Epimers in Vacuo and Solution. ACS OMEGA 2018; 3:16899-16915. [PMID: 31458314 PMCID: PMC6643604 DOI: 10.1021/acsomega.8b02213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/07/2018] [Indexed: 05/12/2023]
Abstract
Density functional theory (DFT) is a widely used methodology for the computation of molecular and electronic structure, and we confirm that B3LYP and the high-level ab initio G3B3 method are in excellent agreement for the lowest-energy isomers of the 16 glucose epimers. Density-functional tight-binding (DFTB) is an approximate version of DFT with typically comparable accuracy that is 2 to 3 orders of magnitude faster, therefore generally very suitable for processing large numbers of complex structures. Conformational isomerism in sugars is well known to give rise to a large number of isomer structures. On the basis of a comprehensive study of glucose epimers in vacuo and aqueous solution, we found that the performance of DFTB is on par to B3LYP in terms of geometrical parameters excluding hydrogen bonds and isomer energies. However, DFTB underestimates both hydrogen bonding interactions as well as torsional barriers associated with rotations of the hydroxy groups, resulting in a counterintuitive overemphasis of hydrogen bonding in both gas phase as well as in water. Although the associated root mean squared deviation from B3LYP within epimer isomer groups is only on the order of 1 kcal/mol, this deviation affects the correct assignment of major isomer ordering, which span less than 10 kcal/mol. Both second- as well as third-order DFTB methods are exhibiting similar deviations from B3LYP. Even after the inclusion of empirical dispersion corrections in vacuum, these deviations remain for a large majority of isomer energies and geometries when compared to dispersion-corrected B3LYP.
Collapse
Affiliation(s)
- Ka Hung Lee
- Department
of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
- Bredesen
Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Udo Schnupf
- Department
of Chemistry and Biochemistry, Bradley University, Peoria, Illinois 61625, United States
- E-mail: (U.S.)
| | - Bobby G. Sumpter
- Computational Sciences and Engineering Division &
Chemical Sciences
Division and Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Stephan Irle
- Department
of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
- Computational Sciences and Engineering Division &
Chemical Sciences
Division and Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- E-mail: (S.I.)
| |
Collapse
|
10
|
Vickman AE, Pohl NLB. Probing deoxysugar conformational preference: A comprehensive computational study investigating the effects of deoxygenation. Carbohydr Res 2018; 475:17-26. [PMID: 30771703 DOI: 10.1016/j.carres.2018.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/26/2018] [Accepted: 12/06/2018] [Indexed: 10/27/2022]
Abstract
Deoxysugars are intrinsic components in a number of antibiotics, antimicrobials, and therapeutic agents that often dictate receptor binding, improve efficacy, and provide a diverse toolbox in modifying glycoconjugate function due to an extensive number of unique isomers and inherent conformational flexibility. Hence, this work provides a comprehensive examination of the conformational effects associated with deoxygenation of the pyranose ring. Both the location and degree of deoxygenation were evaluated by interrogating the energetic landscape for a number of mono- and dideoxyhexopyranose derivatives using DFT methods (M05-2X/cc-pVTZ(-f)). Both anomeric forms and in some cases, the alternate chair form, have been investigated in the gas phase. As was documented in a preceding study, variation of the C-6 oxidation state has been shown to affect the anomeric preference of select glucose stereoisomers. Similar results were also observed for several deoxysugar isomers in this work, wherein the alternate anomer was favored upon reduction to the 6-deoxyhexose derivative or oxidation to the hexonic acid. Additionally, comparison of relative Gibbs free energies revealed C-3 deoxygenation imparts greater instability compared to C-2 or C-4 deoxygenation, as indicated by an increase in free energy for 3-deoxysugars. A polarizable continuum solvation model was also applied to empirically validate theoretical results for several deoxysugars, wherein good agreement with both carbon (σ = 1.6 ppm) and proton (σ = 0.20 ppm) NMR shifts was observed for the majority of isomers. Solvated and gas phase anomeric ratios were also calculated and compared favorably to reported literature values, although some discrepancies are noted.
Collapse
Affiliation(s)
- Alison E Vickman
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Nicola L B Pohl
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
| |
Collapse
|
11
|
Tanaka S, Kojić D, Tsenkova R, Yasui M. Quantification of anomeric structural changes of glucose solutions using near-infrared spectra. Carbohydr Res 2018; 463:40-46. [PMID: 29763789 DOI: 10.1016/j.carres.2018.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/16/2018] [Accepted: 04/24/2018] [Indexed: 10/16/2022]
Abstract
Glucose is the most abundant carbohydrate found in living organisms. It exists as two anomers: α-D-glucose and β-D-glucose, which differ in how the hydroxyl group on the C1 carbon is directed. In solutions, the ratio between α- and β-D-glucose is typically 4:6 but can vary depending on the surrounding ions or temperature. In this study, we obtained near-infrared (NIR) spectra of the glucose anomers based on concentration, and analyzed the spectral difference between each anomer by spectra subtraction and principal component analysis, respectively. Moreover, by simultaneously measuring the optical rotation and NIR spectra from dissolution to equilibration, we showed that NIR spectra quantitatively estimated the specific rotations of glucose solutions using partial least-squares regression in the 1100-1800 nm wavelength range. All the analytical results indicated that the absorption at 1742 nm possess the potential to distinguish each glucose anomer quantitatively. Therefore, we addressed the prediction of the specific rotation by the absorption at 1742 nm, and demonstrated that the absorption normalized by line subtraction showed the high correlation with measured specific rotation. The absorption at 1742 nm reflects structural changes of the glucose anomers in solution. Our spectroscopy study not only provides spectral information about glucose anomers, which are the most fundamental chemical compounds in organisms, but also shows the possibility to detect the anomer ratio in vivo for the fields of agriculture and medicine by taking advantage of NIR.
Collapse
Affiliation(s)
- Sae Tanaka
- Department of Pharmacology, Keio University School of Medicine, 160-8582, Japan; Keio Advanced Research Center for Water Biology and Medicine, Keio University, 108-8345, Japan.
| | - Dušan Kojić
- Department of Pharmacology, Keio University School of Medicine, 160-8582, Japan; Keio Advanced Research Center for Water Biology and Medicine, Keio University, 108-8345, Japan
| | - Roumiana Tsenkova
- Keio Advanced Research Center for Water Biology and Medicine, Keio University, 108-8345, Japan; Department of Agricultural Engineering and Socio-Economics, Kobe University, 657-8501, Japan
| | - Masato Yasui
- Department of Pharmacology, Keio University School of Medicine, 160-8582, Japan; Keio Advanced Research Center for Water Biology and Medicine, Keio University, 108-8345, Japan; Keio Global Research Institute, 108-8345, Japan
| |
Collapse
|
12
|
Tomobe K, Yamamoto E, Yasui M, Yasuoka K. Effects of temperature, concentration, and isomer on the hydration structure in monosaccharide solutions. Phys Chem Chem Phys 2018; 19:15239-15246. [PMID: 28569306 DOI: 10.1039/c7cp02392h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Water-monosaccharide coupled interactions are essential for the function, stability, and dynamics of all glycans. Using molecular dynamics simulations, we investigated the effects of temperature, concentration, and monosaccharide isomer on the hydration structure and water dynamics in the hydration shell of monosaccharides in solution. We found that perturbations of the hydrogen-bond (H-bond) network in the first hydration shell around each monosaccharide molecule can be separated into two regions: one rich in water molecules with donor H-bonds (in the 2.4-2.8 Å region) and the other rich in water molecules with abundant acceptor H-bonds (in the 2.8-3.3 Å region). Moreover, we investigated the dependencies of clustering and conversion of the conformers of the monosaccharides on temperature and concentration. Increasing the concentration enhances monosaccharide clustering in all the monosaccharide solutions, while cluster formation does not depend on temperature. In the clusters, some water molecules in the hydration shell are replaced with monosaccharide oxygen atoms, which contributes to the shrinkage of the hydration shell with increasing monosaccharide concentration. The monosaccharides basically adopt one of two conformers, the stable chair or the unstable boat conformer. We revealed that the hydration structures of the boat and chair conformers were dramatically different. As the temperature increases, the content of the chair conformer decreases. Thus, the conversion of conformers strongly affects the hydration structure around the monosaccharide. These results are critical to understand the important roles of the hydration structure in glycan solutions.
Collapse
Affiliation(s)
- Katsufumi Tomobe
- Department of Mechanical Engineering, Keio University, Yokohama, 223-8522, Japan.
| | | | | | | |
Collapse
|
13
|
Bestaoui-Berrekhchi-Berrahma N, Springborg M, Berrekhchi-Berrahma C, Sekkal-Rahal M. DFT and MP2 conformational study of 3,6-anhydro-α-d-galactose in gas phase and in aqueous solvent. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
14
|
Arifin, Yokogawa D, Schnupf U, Irle S. Statistical Mechanics-Based Theoretical Investigation of Solvation Effects on Glucose Anomer Preferences. J Phys Chem B 2018; 122:290-296. [PMID: 29271652 DOI: 10.1021/acs.jpcb.7b10270] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The importance of solvation effects on the stability of glucose anomers has been studied by the combination of quantum mechanics and statistical mechanics, namely, the reference interaction site model self-consistent field spatial electron density distribution. The preferences of α- and β-glucose in H2O are well reproduced with the obtained ratio of 35:65 for α- and β-glucose, respectively. Indirect interactions and bulk effects, described by the Onsager model, are relatively small compared to the direct solute-solvent interactions, especially in [DMIM]Cl and dimethyl sulfoxide. From the decomposition of solvation free energy and solvation structures, it can be seen that the interactions with the solvent molecules greatly contribute to the anomer preferences.
Collapse
Affiliation(s)
- Arifin
- Department of Chemistry, Graduate School of Science, Nagoya University , Chikusa, Nagoya 464-8601, Japan.,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University , Chikusa, Nagoya 464-8602, Japan
| | - Daisuke Yokogawa
- Department of Chemistry, Graduate School of Science, Nagoya University , Chikusa, Nagoya 464-8601, Japan.,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University , Chikusa, Nagoya 464-8602, Japan
| | - Udo Schnupf
- Mund-Lagowski Department of Chemistry & Biochemistry, Bradley University , Peoria 61625, Illinois, United States
| | - Stephan Irle
- Department of Chemistry, Graduate School of Science, Nagoya University , Chikusa, Nagoya 464-8601, Japan.,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University , Chikusa, Nagoya 464-8602, Japan
| |
Collapse
|
15
|
Plazinski W, Plazinska A. Molecular dynamics simulations of hexopyranose ring distortion in different force fields. PURE APPL CHEM 2017. [DOI: 10.1515/pac-2016-0922] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract:The four classical, biomolecular force fields designed to study hexopyranose-based carbohydrates (GROMOS 56a6CARBO/56a6CARBO_R, GROMOS 53a6GLYC, CHARMM and GLYCAM06) have been tested in the context of ring-inversion properties. These properties were evaluated for both unfunctionalized monomers of all hexopyranoses of the d series and for residues in a chain composed of uniform units connected by α(1→4) and β(1→4) glycosidic linkages. The results indicate that the tested force fields differ in their predictions of the ring-inversion properties of both monomers and residues in a chain. The comparison with the available experimental data and with the semi-empirical Angyal scheme reveals that, at the level of monomers, GROMOS 56a6CARBO, GROMOS 53a6GLYC and CHARMM correctly reproduce the ring-inversion free energies. However, due to the lack of analogous reference data we cannot state which force field is more or less accurate in the context of ring distortion of residues in a chain. Therefore, the use of ab initio potentials is recommended in the prospective, quantitative studies on the related subject.
Collapse
Affiliation(s)
- Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Cracow, Poland, Tel.: +48815375685, Fax: +48815375685, e-mail:
| | - Anita Plazinska
- Department of Biopharmacy, Faculty of Pharmacy, Medical University of Lublin, W. Chodzki Str., 4a, 20-093 Lublin, Poland
| |
Collapse
|
16
|
Del Vigo EA, Marino C, Stortz CA. Exhaustive rotamer search of the 4C1 conformation of α- and β-d-galactopyranose. Carbohydr Res 2017; 448:136-147. [DOI: 10.1016/j.carres.2017.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/03/2017] [Accepted: 05/05/2017] [Indexed: 10/19/2022]
|
17
|
Dissecting the role of dispersion on the quantum topology phase diagram of monosaccharide isomers. MONATSHEFTE FUR CHEMIE 2017. [DOI: 10.1007/s00706-016-1869-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
18
|
Effects of varying the 6-position oxidation state of hexopyranoses: a systematic comparative computational analysis of 48 monosaccharide stereoisomers. J Mol Model 2017; 23:214. [PMID: 28656484 DOI: 10.1007/s00894-017-3385-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/04/2017] [Indexed: 01/25/2023]
Abstract
Knowledge of multi-dimensional carbohydrate structure is essential when delineating structure-function relationships in the development of analytical techniques such as ion mobility-mass spectrometry and of carbohydrate-based therapeutics, as well as in rationally modifying the chemical and physical properties of drugs and materials based on sugars. Although monosaccharides are conventionally presumed to adopt the canonical 4C1 chair conformation, it is not well known how altering the substituent identity around the pyranose ring affects the favored conformational state. This work provides a comprehensive and systematic computational comparison of all eight aldohexose isomers in the gas phase with reduction and oxidation at the C-6 position using density functional theory (M05-2X/cc-pVTZ(-f)//B3LYP/6-31G**) to determine the conformational and anomeric preference for each sugar in the gas phase. All 6-deoxyhexose and aldohexose isomers favored the 4C1 chair conformation, while oxidation at C-6 showed a shift in equilibrium to favor the 1C4 chair for β-alluronic acid, β-guluronic acid, and β-iduronic acid. The anomeric preference was found to be significantly affected by a remote change in oxidation state, with the alternate anomer favored for several isomers. These findings provide a fundamental platform to empirically test steric and electronic effects of pyranose substituents, with the goal of formulating straightforward rules that govern carbohydrate reactivity and drive quicker, more efficient syntheses. Graphical abstract A systematic comparative conformational analysis of all eight aldohexose isomers using DFT methods (M05-2X/cc-pVTZ(-f)) reveals changes in anomeric and ring conformational preference upon reduction or oxidation at the C-6 position for several sugars.
Collapse
|
19
|
Anomeric proportions of d -glucopyranose at the equilibrium determined from 1 H-NMR spectra I. Investigation of experimental conditions and concentration dependence at 25.0 °C. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.02.062] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
20
|
Satoh H, Oda T, Nakakoji K, Uno T, Tanaka H, Iwata S, Ohno K. Potential Energy Surface-Based Automatic Deduction of Conformational Transition Networks and Its Application on Quantum Mechanical Landscapes of d-Glucose Conformers. J Chem Theory Comput 2016; 12:5293-5308. [PMID: 27673598 DOI: 10.1021/acs.jctc.6b00439] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper describes our approach that is built upon the potential energy surface (PES)-based conformational analysis. This approach automatically deduces a conformational transition network, called a conformational reaction route map (r-map), by using the Scaled Hypersphere Search of the Anharmonic Downward Distortion Following method (SHS-ADDF). The PES-based conformational search has been achieved by using large ADDF, which makes it possible to trace only low transition state (TS) barriers while restraining bond lengths and structures with high free energy. It automatically performs sampling the minima and TS structures by simply taking into account the mathematical feature of PES without requiring any a priori specification of variable internal coordinates. An obtained r-map is composed of equilibrium (EQ) conformers connected by reaction routes via TS conformers, where all of the reaction routes are already confirmed during the process of the deduction using the intrinsic reaction coordinate (IRC) method. The postcalculation analysis of the deduced r-map is interactively carried out using the RMapViewer software we have developed. This paper presents computational details of the PES-based conformational analysis and its application to d-glucose. The calculations have been performed for an isolated glucose molecule in the gas phase at the RHF/6-31G level. The obtained conformational r-map for α-d-glucose is composed of 201 EQ and 435 TS conformers and that for β-d-glucose is composed of 202 EQ and 371 TS conformers. For the postcalculation analysis of the conformational r-maps by using the RMapViewer software program we have found multiple minimum energy paths (MEPs) between global minima of 1C4 and 4C1 chair conformations. The analysis using RMapViewer allows us to confirm the thermodynamic and kinetic predominance of 4C1 conformations; that is, the potential energy of the global minimum of 4C1 is lower than that of 1C4 (thermodynamic predominance) and that the highest energy of those of all the TS structures along a route from 4C1 to 1C4 is lower than that of 1C4 to 4C1 (kinetic predominance).
Collapse
Affiliation(s)
- Hiroko Satoh
- Research Organization of Information and Systems (ROIS), Tokyo 105-0001, Japan.,Department of Chemistry, University of Zurich , 8057 Zurich, Switzerland.,National Institute of Informatics (NII), Tokyo 101-8430, Japan.,Institute for Quantum Chemical Exploration (IQCE), Tokyo 108-0022, Japan
| | - Tomohiro Oda
- Software Research Associates Inc., Tokyo 171-8513, Japan
| | - Kumiyo Nakakoji
- Center for the Promotion of Interdisciplinary Education and Research, Kyoto University , Kyoto 606-8501, Japan
| | - Takeaki Uno
- National Institute of Informatics (NII), Tokyo 101-8430, Japan
| | - Hiroaki Tanaka
- Department of Mathematical Informatics, University of Tokyo , Tokyo 113-8654, Japan
| | - Satoru Iwata
- Department of Mathematical Informatics, University of Tokyo , Tokyo 113-8654, Japan
| | - Koichi Ohno
- Institute for Quantum Chemical Exploration (IQCE), Tokyo 108-0022, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University , Sendai 980-8578, Japan
| |
Collapse
|
21
|
A new hybrid (experimental–theoretical) quantitative method for detection of relative anomer concentrations in water. Struct Chem 2015. [DOI: 10.1007/s11224-015-0722-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
22
|
Plazinski W, Lonardi A, Hünenberger PH. Revision of the GROMOS 56A6(CARBO) force field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains. J Comput Chem 2015; 37:354-65. [PMID: 26525424 DOI: 10.1002/jcc.24229] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 10/03/2015] [Accepted: 10/06/2015] [Indexed: 01/19/2023]
Abstract
This article describes a revised version 56A6(CARBO_R) of the GROMOS 56A6(CARBO) force field for hexopyranose-based carbohydrates. The simulated properties of unfunctionalized hexopyranoses are unaltered with respect to 56A6CARBO . In the context of both O1 -alkylated hexopyranoses and oligosaccharides, the revision stabilizes the regular (4) C1 chair for α-anomers, with the opposite effect for β-anomers. As a result, spurious ring inversions observed in α(1→4)-linked chains when using the original 56A6(CARBO) force field are alleviated. The (4) C1 chair is now the most stable conformation for all d-hexopyranose residues, irrespective of the linkage type and anomery, and of the position of the residue along the chain. The methylation of a d-hexopyranose leads to a systematic shift in the ring-inversion free energy ((4) C1 to (1) C4 ) by 7-8 kJ mol(-1), positive for the α-anomers and negative for the β-anomers, which is qualitatively compatible with the expected enhancement of the anomeric effect upon methylation at O1. The ring-inversion free energies for residues within chains are typically smaller in magnitude compared to those of the monomers, and correlate rather poorly with the latter. This suggests that the crowding of ring substituents upon chain formation alters the ring flexibility in a nonsystematic fashion. In general, the description of carbohydrate chains afforded by 56A6(CARBO_R) suggests a significant extent of ring flexibility, i.e., small but often non-negligible equilibrium populations of inverted chairs, and challenges the "textbook" picture of conformationally locked carbohydrate rings.
Collapse
Affiliation(s)
- Wojciech Plazinski
- Laboratory of Physical Chemistry, ETH Hönggerberg, HCI, Zürich, CH-8093, Switzerland.,J. Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Ul. Niezapominajek 8, Cracow, 30-239, Poland
| | - Alice Lonardi
- Laboratory of Physical Chemistry, ETH Hönggerberg, HCI, Zürich, CH-8093, Switzerland
| | | |
Collapse
|
23
|
Szczepaniak M, Moc J. Tautomers of Gas-Phase Erythrose and Their Interconversion Reactions: Insights from High-Level ab Initio Study. J Phys Chem A 2015; 119:10946-58. [DOI: 10.1021/acs.jpca.5b07720] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marek Szczepaniak
- Faculty
of Chemistry, Wroclaw University, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| | - Jerzy Moc
- Faculty
of Chemistry, Wroclaw University, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| |
Collapse
|
24
|
|
25
|
Kosaka A, Aida M, Katsumoto Y. Reconsidering the activation entropy for anomerization of glucose and mannose in water studied by NMR spectroscopy. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.03.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
26
|
Abstract
The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.
Collapse
Affiliation(s)
- Serge Pérez
- Department of Molecular Pharmacochemistry, CNRS, University Grenoble-Alpes, Grenoble, France.
| | - Igor Tvaroška
- Department of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic; Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University, Nitra, Slovak Republic.
| |
Collapse
|
27
|
Karabulut S, Leszczynski J. Molecular structure of aurothioglucose: a comprehensive computational study. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
28
|
Morris MJ, Striegel AM. Determining the solution conformational entropy of oligosaccharides by SEC with on-line viscometry detection. Carbohydr Polym 2014; 106:230-7. [DOI: 10.1016/j.carbpol.2014.02.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 02/07/2014] [Accepted: 02/08/2014] [Indexed: 11/30/2022]
|
29
|
Does the “C3effect” offset the Δ2 effect, as regards the solution flexibility of aldoses? Biopolymers 2014; 101:703-11. [DOI: 10.1002/bip.22446] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 10/23/2013] [Accepted: 11/15/2013] [Indexed: 02/06/2023]
|
30
|
Patel DS, He X, MacKerell AD. Polarizable empirical force field for hexopyranose monosaccharides based on the classical Drude oscillator. J Phys Chem B 2014; 119:637-52. [PMID: 24564643 PMCID: PMC4143499 DOI: 10.1021/jp412696m] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A polarizable empirical force field based on the classical Drude oscillator is presented for the hexopyranose form of selected monosaccharides. Parameter optimization targeted quantum mechanical (QM) dipole moments, solute-water interaction energies, vibrational frequencies, and conformational energies. Validation of the model was based on experimental data on crystals, densities of aqueous-sugar solutions, diffusion constants of glucose, and rotational preferences of the exocylic hydroxymethyl of d-glucose and d-galactose in aqueous solution as well as additional QM data. Notably, the final model involves a single electrostatic model for all sixteen diastereomers of the monosaccharides, indicating the transferability of the polarizable model. The presented parameters are anticipated to lay the foundation for a comprehensive polarizable force field for saccharides that will be compatible with the polarizable Drude parameters for lipids and proteins, allowing for simulations of glycolipids and glycoproteins.
Collapse
Affiliation(s)
- Dhilon S Patel
- Department of Pharmaceutical Sciences, University of Maryland , 20 Penn Street HSF II, Baltimore, Maryland 21201, United States
| | | | | |
Collapse
|
31
|
DFT optimization and DFT-MD studies of glucose, ten explicit water molecules enclosed by an implicit solvent, COSMO. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2013.12.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
32
|
Mayes HB, Tian J, Nolte MW, Shanks BH, Beckham GT, Gnanakaran S, Broadbelt LJ. Sodium ion interactions with aqueous glucose: insights from quantum mechanics, molecular dynamics, and experiment. J Phys Chem B 2013; 118:1990-2000. [PMID: 24308866 DOI: 10.1021/jp409481f] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In the last several decades, significant efforts have been conducted to understand the fundamental reactivity of glucose derived from plant biomass in various chemical environments for conversion to renewable fuels and chemicals. For reactions of glucose in water, it is known that inorganic salts naturally present in biomass alter the product distribution in various deconstruction processes. However, the molecular-level interactions of alkali metal ions and glucose are unknown. These interactions are of physiological interest as well, for example, as they relate to cation-glucose cotransport. Here, we employ quantum mechanics (QM) to understand the interaction of a prevalent alkali metal, sodium, with glucose from a structural and thermodynamic perspective. The effect on β-glucose is subtle: a sodium ion perturbs bond lengths and atomic partial charges less than rotating a hydroxymethyl group. In contrast, the presence of a sodium ion significantly perturbs the partial charges of α-glucose anomeric and ring oxygens. Molecular dynamics (MD) simulations provide dynamic sampling in explicit water, and both the QM and the MD results show that sodium ions associate at many positions with respect to glucose with reasonably equivalent propensity. This promiscuous binding nature of Na(+) suggests that computational studies of glucose reactions in the presence of inorganic salts need to ensure thorough sampling of the cation positions, in addition to sampling glucose rotamers. The effect of NaCl on the relative populations of the anomers is experimentally quantified with light polarimetry. These results support the computational findings that Na(+) interacts similarly with α- and β-glucose.
Collapse
Affiliation(s)
- Heather B Mayes
- Department of Chemical and Biological Engineering, Northwestern University , Evanston, Illinois 60208, United States
| | | | | | | | | | | | | |
Collapse
|
33
|
Karabulut S, Leszczynski J. Anomeric and rotameric preferences of glucopyranose in vacuo, water and organic solvents. J Mol Model 2013; 19:3637-45. [DOI: 10.1007/s00894-013-1902-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 05/27/2013] [Indexed: 11/28/2022]
|
34
|
Taha HA, Richards MR, Lowary TL. Conformational Analysis of Furanoside-Containing Mono- and Oligosaccharides. Chem Rev 2012; 113:1851-76. [DOI: 10.1021/cr300249c] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hashem A. Taha
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Michele R. Richards
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Todd L. Lowary
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| |
Collapse
|
35
|
Matsuo K, Namatame H, Taniguchi M, Gekko K. Vacuum-ultraviolet electronic circular dichroism study of methyl α-D-glucopyranoside in aqueous solution by time-dependent density functional theory. J Phys Chem A 2012; 116:9996-10003. [PMID: 22950837 DOI: 10.1021/jp306914s] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The vacuum-ultraviolet (VUV) electronic circular dichroism (ECD) spectrum of methyl α-D-glucopyranoside (methyl α-D-Glc) was measured down to 163 nm in aqueous solution using a synchrotron-radiation VUV-ECD spectrophotometer. The spectrum exhibited two characteristic ECD peaks around 170 nm, which depend on the trans (T) and gauche (G) configurations of the hydroxymethyl group at C-5. To elucidate the influences of the T and G configurations on the spectrum, the ECD spectra of three rotamers (α-GT, α-GG, and α-TG) of methyl α-D-Glc were calculated using time-dependent density functional theory (TDDFT) combined with molecular dynamics simulation. A linear combination of the ECD spectra of these three rotamers, which differ markedly from each other, produced a methyl α-D-Glc spectrum similar to that observed experimentally. The spectrum was assignable to the n-σ* transitions of the ring oxygen and methoxy oxygen with minor contributions from the hydroxyl oxygen. The differences in α-GT, α-GG, and α-TG spectra were attributed to fluctuations of the configurations of the hydroxymethyl group at C-5 and the hydroxyl group at C-4, which strongly affected the orientations of intramolecular hydrogen bonds around the ring oxygen. These findings demonstrate that combining VUV-ECD and TDDFT is useful for structural characterization of saccharides in aqueous solution.
Collapse
Affiliation(s)
- Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima 739-0046, Japan.
| | | | | | | |
Collapse
|
36
|
Azofra LM, Alkorta I, Elguero J, Popelier PL. Conformational study of the open-chain and furanose structures of d-erythrose and d-threose. Carbohydr Res 2012; 358:96-105. [DOI: 10.1016/j.carres.2012.06.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 06/18/2012] [Accepted: 06/19/2012] [Indexed: 10/28/2022]
|
37
|
Sameera WMC, Pantazis DA. A Hierarchy of Methods for the Energetically Accurate Modeling of Isomerism in Monosaccharides. J Chem Theory Comput 2012; 8:2630-45. [PMID: 26592108 DOI: 10.1021/ct3002305] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- W. M. C. Sameera
- Institut Català d’Investigació
Química, Av. Països Catalans 16, 43007 Tarragona, Spain
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für
Bioanorganische Chemie, Stiftstrasse 34-36, 45470 Mülheim an
der Ruhr, Germany
| |
Collapse
|
38
|
Sattelle BM, Bose-Basu B, Tessier M, Woods RJ, Serianni AS, Almond A. Dependence of pyranose ring puckering on anomeric configuration: methyl idopyranosides. J Phys Chem B 2012; 116:6380-6. [PMID: 22577942 DOI: 10.1021/jp303183y] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the aldohexopyranose idose, the unique presence of three axial ring hydroxyl groups causes considerable conformational flexibility, rendering it challenging to study experimentally and an excellent model for rationalizing the relationship between puckering and anomeric configuration. Puckering in methyl α- and β-L-idopyranosides was predicted from kinetically rigorous 10 μs simulations using GLYCAM11 and three explicit water models (TIP3P, TIP4P, and TIP4P-EW). In each case, computed pyranose ring three-bond (vicinal) (1)H-(1)H spin couplings ((3)J(H,H)) trended with NMR measurements. These values, calculated puckering exchange rates and free energies, were independent of the water model. The α- and β-anomers were (1)C(4) chairs for 85 and >99% of their respective trajectories and underwent (1)C(4)→(4)C(1) exchange at rates of 20 μs(-1) and 1 μs(-1). Computed α-anomer (1)C(4)↔(4)C(1) puckering rates depended on the exocyclic C6 substituent, comparing hydroxymethyl with carboxyl from previous work. The slower kinetics and restricted pseudorotational profile of the β-anomer were caused by water occupying a cavity bounded by the anomeric 1-O-methyl and the C6 hydroxymethyl groups. This finding rationalizes the different methyl α- and β-L-idopyranoside (3)J(H,H) values. Identifying a relationship between idopyranose anomeric configuration, microsecond puckering, and water structure facilitates engineering of biologically and commercially important derivatives and underpins deciphering presently elusive structure-function relationships in the glycome.
Collapse
Affiliation(s)
- Benedict M Sattelle
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | | | | | | | | | | |
Collapse
|
39
|
Andrade RR, da Silva CO. Specific rotation as a property to validate monosaccharide conformations. Carbohydr Res 2012; 350:62-7. [PMID: 22281178 DOI: 10.1016/j.carres.2011.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 11/28/2011] [Accepted: 12/13/2011] [Indexed: 11/15/2022]
Abstract
Specific rotation ([α](D)) values were calculated for the 15 conformations of xylopyranose that are the most stable in the gas phase and in aqueous solution. The effects of different theoretical descriptions and the medium on the geometry of the conformers and the [α](D) values are evaluated. Differences in [α](D) values found for the same conformer in all descriptions used were smaller than those found between any two different conformers in the same description. The difference between [α](D) values is prominent, even for two conformations that are distinguished from each other only by the orientation of one secondary hydroxyl group. This finding suggests that [α](D) values may potentially be used in the validation of monosaccharide conformations that are theoretically sampled.
Collapse
Affiliation(s)
- Renato R Andrade
- Departamento de Química, Universidade Federal Rural do Rio de Janeiro, km 47-Seropédica, Rio de Janeiro, Brazil
| | | |
Collapse
|
40
|
Alkorta I, Popelier PLA. Computational study of mutarotation in erythrose and threose. Carbohydr Res 2011; 346:2933-9. [DOI: 10.1016/j.carres.2011.10.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 10/05/2011] [Accepted: 10/07/2011] [Indexed: 11/26/2022]
Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3, 28006-Madrid, Spain.
| | | |
Collapse
|
41
|
Vrančić C, Petrich W. Effective Fragment Potential Study of the Influence of Hydration on the Vibrational Spectrum of Glucose. J Phys Chem A 2011; 115:12373-9. [DOI: 10.1021/jp207225k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christian Vrančić
- Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
| | - Wolfgang Petrich
- Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
| |
Collapse
|
42
|
Guan CZ, Chen T, Wu JY, Chen Q, Wang D, Stang PJ, Wan LJ. Surface-confined conformers and coassembly-induced conformer resolution. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:9994-9999. [PMID: 21721510 DOI: 10.1021/la202076z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Stereoisomerism is a fundamental chemistry issue and has been intensively investigated because of its importance in organic chemistry, biology, and pharmacology. Molecules with freely rotatable single bonds have many interconvertable conformers. Herein, we report the surface-adsorption-induced conformer resolution by employing azobenzene-3,3-dicarboxylic acid (ADA-33) as a model compound. Two linear assembly phases composed of trans conformers on a highly oriented pyrolytic graphite (HOPG) surface are observed by scanning tunneling microscopy. With the codeposition with 1-octanoic acid (OA), only one trans conformer of ADA-33 can be recognized by OA to form a two-component assembly with alternately arranged ADA-33 and OA stripes, which can be attributed to the epitaxial assembly of ADA-33 and OA on the HOPG surface, and weak hydrogen bonding exists between conformer I and OA molecules. The results are of significance with respect to the discrimination and resolution of conformers on a solid surface and provide molecular insights into the coadsorption assembly on the surface.
Collapse
Affiliation(s)
- Cui-Zhong Guan
- Institute of Chemistry, Chinese Academy of Sciences, and Beijing National Laboratory for Molecular Sciences, Beijing 100190, China
| | | | | | | | | | | | | |
Collapse
|
43
|
Linear free energy relationship for the anomeric effect: MP2, DFT and ab initio study of 2-substituted-1,4-dioxanes. Carbohydr Res 2011; 346:1047-56. [DOI: 10.1016/j.carres.2011.03.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 02/20/2011] [Accepted: 03/09/2011] [Indexed: 11/23/2022]
|
44
|
Momany FA, Schnupf U. DFTMD studies of β-cellobiose: conformational preference using implicit solvent. Carbohydr Res 2011; 346:619-30. [PMID: 21333280 DOI: 10.1016/j.carres.2011.01.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 01/04/2011] [Accepted: 01/06/2011] [Indexed: 10/18/2022]
Abstract
Previous DFT in vacuo studies on the conformational preferences for cellobiose showed that upon optimization the φ(H)-anti conformations were of lower energy than the syn forms. Upon optimization using an implicit solvation method, COSMO, the syn or observed form was still not predicted to be of lower energy than the φ(H)-anti form, even though optimization after addition of several explicit water molecules did show a relative energy difference favoring the syn form. In order to examine the predictive ability of COSMO on this carbohydrate, constant energy dynamics, DFTMD, simulations were carried out on low energy syn and φ(H)-anti conformations with and without COSMO included during the dynamics. The resulting analysis confirmed that when COSMO is included in the dynamics, the syn conformations become energetically favored over the φ(H)-anti forms suggesting that both solvent and entropy play roles in dictating the solution conformation of cellobiose. Analysis of the dynamic runs includes distributions of selected dihedral angles versus time, conformational transitions, and populations of some quasi-planar, boat, skew forms during the simulations.
Collapse
Affiliation(s)
- F A Momany
- Plant Polymer Research, USDA, ARS, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, IL 61604, USA.
| | | |
Collapse
|
45
|
Taha HA, Roy PN, Lowary TL. Theoretical Investigations on the Conformation of the β-d-Arabinofuranoside Ring. J Chem Theory Comput 2010; 7:420-32. [DOI: 10.1021/ct100450s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hashem A. Taha
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2 and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Pierre-Nicholas Roy
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2 and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Todd L. Lowary
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2 and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| |
Collapse
|
46
|
Autieri E, Sega M, Pederiva F, Guella G. Puckering free energy of pyranoses: A NMR and metadynamics-umbrella sampling investigation. J Chem Phys 2010; 133:095104. [DOI: 10.1063/1.3476466] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
47
|
|